The identification result of MAP-Match and conventional method
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ABSTRACT: The comparison of GPSMs that's identified by StrucGP in 24 MouseBrain raw files, using MAP-Match and the conventional calibration method saparately.
Project description:In this study, we applied the recently developed software, StrucGP to large-scale characterize glycoproteins, and IGPs, as well as precise site-specific glycan structures in human spermatozoa. Furthermore, bioinformatical analyses were conducted to systematically describe the potential functions of N-glycosylation in human spermatozoa.
Project description:In this project we developed a new algorithm termed StrucGP, for large-scale interpretation of N-glycan structures on intact glycopeptides from tandem mass spectrometry data. StrucGP is able to reveal the glycan structure heterogeneity for individual glycosites. The StrucGP also has high performance in distinguishing various structure isoforms and identifying new and rare glycan structures from complex samples.
Project description:In this study, we performed site-specific N-glycoproteomic analysis of THP-1 derived four M2 macrophage subtypes (M2a, M2b, M2c, and M2d) by StrucGP method combined with 2D-LC-MS/MS analysis, and revealed the distribution regularities and characters of N-glycans.
Project description:Spike (S) protein plays a key role in COVID-19 (SARS-CoV-2) infection and host-cell entry. Previous studies have systematically analyzed site-specific glycans compositions of S protein. Here, we further provide structure-clear N-glycosylation of S protein at site-specific level by using our recently developed structure- and site-specific N-glycoproteomics sequencing algorithm StrucGP. In addition to the common N-glycans as detected in previous studies, many uncommon glycosylation structures such as LacdiNAc structures, Lewis structures, Mannose 6-Phosphate (M6P) residues and bisected core structures were unambiguously mapped at a total of 20 glycosites in the S protein trimer and protomer. These data further supports the glycosylation structural-functional investigations of COVID-19 virus Spike.
Project description:In this study, we used human THP-1-derived macrophages as an immune cell model, and systematically performed glycoproteomics of three subtypes of macrophages by StrucGP.To study the N‑Glycoproteomic of them, the intact glycopeptides were first enriched and identified using triplicate mass spectrometry (MS)-based glycoproteomic approaches, then StrucGP was used for subsequent analysis. In total three subtypes of macrophages, these intact glycopeptides consist of 253 N-linked glycan structures at 652 unique glycosites from 372 N-glycoproteins, along with their PSM information. A total of 135, 163, and 201 N-glycan structures were identified from M0, M1, and M2 macrophages, respectively.
Project description:Full title: Three-dimensional culture of AIDS-NHL cells influences gene expression related to B-cell development, proliferation and survival The AIDS-NHL-derived cell line, UMCL01-101, representing diffuse large B-cell lymphoma of immunoblastic morphology (AIDS-IBL), was grown in conventional, static suspension culture or three-dimensionally (3D) in the Rotating Wall Vessel (RWV) bioreactor. The objective was to assess the impact on gene expression of growth as a three-dimensional tissue assembly. Global gene expression analysis was performed on UMCL01-101 cells grown under either condition using Affymetrix microarray. UMCL01-101 cells were cultured in the Rotating Wall Vessel bioreactor to form 3D assemblies, or in conventional suspension culture, for 15 days. RNA was prepared from triplicate samples under each growth condition and submitted for microarray analysis.
Project description:High resolution Mass Spectrometry and Peptides identification uncovered ancestral giant insect viruses motifs within Histone-4 peptides in human liver cells. These peptides did not match any human sequence. This finding consolidates the dogma that molecular patterns are universal and suggests that metazoan cellular structures possibly share an evolutionary link with ancient giant viruses.
Project description:Data independent acquistion (DIA) is becoming widely as a method of choice in quantitation proteomics due to its high reproducibility and quantitation accuracy at high-throughput fashion. In this project, we systematically evaluated the effect of the selected precursor mass range for DIA-MS on the protein identification and quantification. We show that a narrow precursor window (400-650 m/z) DIA could identify a 34.7% more proteins than a conventional DIA with a wide precursor window of 400-1200 m/z. When combining the three narrow precursor windows (400-650, 650-900, and 900-1200 m/z) DIA-MS analyses, we obtained a 59.4% increase in the number of proteins quantified than a conventional DIA-MS analysis.
Project description:In this dataset, we investigate the targets of degrasyn in the methicillin-sensitive S. aureus strain NCTC 8325. This includes data on enrichment studies and competition studies with conventional ABPP using a degrasyn-derived probe, competition studies with residue-specific proteomics using the isoDTB-ABPP method and global analysis of protein expression levels in response to degrasyn treatment.